<p>Ubiquitination is a highly conserved and crucial post-translational modification that regulates protein turnover, signal transduction, and stress response in plants. Recent studies have shown that ubiquitination also plays a critical role in regulating secondary metabolism, a key factor in plant defense, environmental adaptation, and developmental transitions. By controlling the stability, activity, and regulatory functions of biosynthetic enzymes, transcription factors, and signaling molecules, ubiquitination dynamically influences metabolic flux and the accumulation of major classes of secondary metabolites. These changes, in turn, affect physiological processes such as the balance between growth and defense, resilience to biotic and abiotic stresses, and ecological interactions. This review consolidates current mechanistic insights into how ubiquitination governs the terpenoid, phenolic, and nitrogen-containing metabolic pathways, emphasizes the functional implications of these regulatory processes for plant performance, and outlines future research directions to link molecular mechanisms with metabolic outputs and plant-level phenotypes.</p>